Unique Drug Repurposing Collection Made Available as Public Resource

Each year, millions of people worldwide suffer from potentially fatal infectious diseases that often leave survivors facing a lifetime of related health problems. But what if drugs against such diseases already existed but nobody knew it?

Scientists at Calibr, a nonprofit drug discovery division of Scripps Research, have exploited an open access collection of existing, safe drug molecules to identify potential candidates against the parasite Cryptosporidium, a major cause of childhood diarrhea in the developing world. The researchers had previously used the drug repositioning screening set, known as ReFRAME (Repurposing, Focused Rescue, and Accelerated Medchem), to identify two compounds that are being tested in clinical trials against Cryptosporidium spp.

In their published paper in The Proceedings of the National Academy of Sciences (PNAS), the team, headed by Arnab Chatterjee, Ph.D., vice president of medicinal chemistry at Calibr, describes the discovery of an additional two compounds that were effective against Cryptosporidium spp in mice, when administered at human-relevant doses.

“ReFRAME was developed as a singular new resource for the global health drug discovery community and is the largest and most comprehensive repurposing collection available,” says Dr. Chatterjee. “ReFRAME takes the concept of accelerating impact on patients through repurposing existing drugs to a new level, offering great potential for finding much-needed therapies more quickly and cost-effectively,” adds Pete Schultz, Ph.D., president and CEO of Scripps Research and Calibr, who is one of the lead researchers on the ReFRAME project. “The drugs we’ve assembled in ReFRAME have already been shown safe in humans, making them an incredibly valuable resource for tackling areas of urgent unmet medical need, especially neglected tropical diseases.”

The Calibr team reports on its latest developments in a paper titled, “The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis.”

The chemical diversity and known safety profiles of drugs that have already been tested in humans make them a particularly “valuable set of compounds to explore potential therapeutic utility in indications outside those originally targeted, especially neglected tropical diseases,” the researchers write. “This practice of ‘drug repurposing’ has become commonplace in academic and other nonprofit drug-discovery efforts, with the appeal that significantly less time and resources are required to advance a candidate into the clinic.” However, what has been lacking, the team comments, is a comprehensive, manageable set of such compounds for screening. There was no single, comprehensive source of samples of the actual drug compounds, which meant repurposing efforts involved collecting thousands of compounds to test against any given disease, which represented a major challenge. The ReFRAME initiative was undertaken to bridge gaps and enable drug repurposing more broadly, they write. “Importantly, the purpose of this collection and the resulting screen data is to accelerate the development of new or existing therapeutics for unmet needs, and to enable public-private partnerships in situations where the drugs are still actively marketed.”

The Calibr researchers started building the currently 12,000 compound ReFRAME library by gathering data on small molecule drugs held in three commercial databases – Clarivate Integrity, GVK Excelra GoStar, and Citeline Pharmprojects – which the industry might use to guide their own R&D and check up on competing drugs. This gave an initial list of about 14,000 compounds, which was then filtered to remove diagnostic agents, chemosensitizers, and other drugs that did not fit the right criteria. The team also trawled through patent filings for additional drug candidates that have been tested in humans, and might represent promising candidates for repurposing. “By combining three different commercial data sets and significant patent intelligence, we identified many unique compounds that have never been collected in one place,” says co-author Jeff Janes, Ph.D., a principal investigator at Calibr.

With list in hand, the researchers then purchased enough of nearly 7,000 of the compounds to allow thousands of screening experiments to be carried out on each. About another 5,000 of the compounds that couldn’t be bought commercially were synthesized by contract research organizations.

Compounds spanning all phases of clinical development are now represented in the collection,” the authors write. “We have generated a library of ∼12,000 high-value compounds composed of purchased or resynthesized FDA-approved drugs (38%), as well as investigational new drugs currently or previously in any phase of clinical development (59%), including 522 noncommercially.

available compounds that represent best guesses of undisclosed structures.” Of particular note, they add, nearly 5,000 of the synthesized compounds are not in any other public collection, and 12% of the chemical structures are not found in PubChem. Containing 12,000 molecules means that the ReFRAME collection size is also manageable for academic labs to screen in cell-based assays in 384- or 1536-well plate formats. “ReFRAME is unique among repurposing collections because of its scale and comprehensiveness, representing a singular resource for the biomedical research community,” the authors comment.

The team focused their reported drug discovery efforts on repurposing drugs in the collection for treating infections by the parasite Cryptosporidium, which is the second-leading cause of life-threatening diarrheal disease in young children, but for which there is only one approved drug, nitazoxanide, which demonstrates only “modest potency,” and is ineffective in patients with compromised immune systems. To date there has been little commercial interest in the parasite, the authors point out, and there are few, if any, validated drug targets. “Therefore, the identification of safe and effective clinically approved molecules for the treatment of infection in young children and immunocompromised populations would be highly advantageous.”

The researchers carried out a high-content screen of Cryptosporidium parvum-infected cells against the ReFRAME library to identify drugs that inhibit the parasite from proliferating. Of 73 resulting hits, the screen yielded two particularly promising novel compounds, VB-201 and ASP-7962, as well as an already FDA-approved leprosy drug clofazimine, which the researchers had previously identified using ReFRAME for potential repurposing. Of the two newly identified compounds, VB-201 is currently being developed as a potential therapeutic for non-alcoholic steatohepatitis and liver fibrosis, atherosclerosis, and other immune-related disorders. ASP-7962 is a best-guess structure of a drug that has been undergoing Phase II clinical testing as an analgesic in osteoarthritis patients.

Encouragingly, the Calibr team’s in vivo tests showed that both VB-201 and ASP-7962 were more effective than nitazoxanide in a mouse model of C. parvum infection. “These two compounds show promise for providing therapeutics for targeting the parasite and not just the symptoms,” comments co-author Case McNamara, Ph.D., a principal investigator at Calibr. “If they prove effective at treating this disease in humans, it could impact the lives of millions of people worldwide.”

The Calibr researchers aim to continue adding compounds to ReFRAME. “Efforts are ongoing to synthesize an additional ~2,000 entries targeted for inclusion as a means of further augmenting the collection and adding compounds that have been advanced into clinical development since the inception of the ReFRAME initiative,” they write. The team hopes to continue to use the resource to identify drugs that can be repurposed as treatments for infections that are common in the developing world. They have also generated an open-access data portal so that the results of their ReFRAME screening experiments can be shared with other researchers to encourage follow-up. “The drug repurposing portal will document ReFRAME’s impact by providing a continuously growing set of highly curated screening data to the scientific community in the area of neglected tropical diseases,” they conclude. Our hope is that by making ReFRAME available as a public resource, we will accelerate the development of new therapies to treat unmet medical needs and provide valuable tool compounds with in vivo activities to reveal new insights into disease biology.”